Self-Assembled Decanethiolate Monolayers on Au(001): Expanding the Family of Known Phases

We have studied decanethiolate self-assembled monolayers on the Au(001) surface. Planar and striped phases, as well as disordered regions, have formed after exposing the Au surface to a decanethiol solution. The planar phases that we observe have a hexagonal symmetry and have not been previously reported for thiols on the Au(001) surface and have lower coverage compared to that of the other known thiol planar phases such as the square α phase. The striped phases that we observe are similar to the previously reported β phase but still feature unit cells that cannot be modeled as the archetype, and the coverage is also somewhat lower. The disordered decanethiolate regions are more dynamic compared to the ordered phases, confirmed with I(t) spectroscopy. This suggests that in these regions the coverage is too low in order to form ordered decanethiolate phases. Our findings contribute to the growing family of possible decanethiol formations on the Au(001) surface, for which still less is known compared to the extensive overview present for the Au(111) surface.


Phase models details and limitations
In this research an RHK scanning probe microscope was deployed. The system uses a beetletype scanner which explains the different orientation of the crystallographic directions on the various STM images presented. Another limitation due to the scanner is the potentially position-dependent stretching/contracting of the measured in-plane lattice parameters. We have performed calibration experiments with a HOPG sample and have found out that with time at a given location, the measured lattice parameters become closer and tend to the expected values. While at the beginning an error up to 20% may be expected, later on the error becomes smaller. Because of the slow relaxation in time, it was not possible to perform full position-dependent calibration. Nevertheless, because all of the images presented were taken after the initial large drift effects were gone, we expect errors less than 20%. This is confirmed by the stretching measured for the width of the hex reconstruction (see the profiles given at the end of the SI), which is at most stretched with 14%, as deduced from the high resolution images which were obtained. In the out-of-plane direction, the apparent height measured showed to be less than expected, a calibration coefficient of about 1.3 was found. This coefficient was already taken into account when plotting the profiles in the last section of this SI.
Because there was no clean Au(001) surface exposed in the close vicinity of the molecular phases, the phases were modeled on top of a square grid which is to represent the unreconstructed Au(001) surface. We took the decision to use tolerances in the x and y directions of the grid up to 10%. Table S1 shows the lattice parameter values deployed for the models in this paper. The values are given as the percentage of the expected in-plane Au(001) lattice parameter of 0.288 nm. These are the values for which we obtained a reasonable agreement between data and model overlay. Of course, especially to account for the complex height variation in the striped phases, more sophisticated models would be required, which take into account the orientation and contribution of the molecular tails. Also, slight incommen-S2 surabilities cannot be easily modeled with this approach. Note, for instance, that changing the tolerances in the table may lead to some deviations in the unit cell labels. This is more relevant for the striped phases as they have a quite large unit cell. For instance, the β phase can be modeled in a similar way as shown in Figure 4(B) in the main text. If we use a lattice parameter in the y-direction of 100% (instead of 90%), for example, the unit cell will become a c(2×22)/(1×11 added row), instead of c(2×24)/(1×12 added row), and the overlap with the experimental data would be still reasonable (some molecule rows only shift slightly from hollow to a bridge site). Therefore, the models we present must be seen as approximations which can only be confirmed with an extensive DFT study, given the unit cells always contain quite many Au atoms.  (001)  Additional STM data

Phase domains
At first we present two domains of the ϕ phase, measured close to each other, shown in Figure S1(A). Clearly a rotation of both ±5 • with respect to the [011] direction is observed.
Due to the square symmetry of the unreconstructed Au(001) substrate, most likely two more domains of this phase exist.
In Figure S1(B) we show a small portion of the ϕ phase (encircled with a dashed shape) close to another planar phase. Below we present a model of this phase too. Due to its S3 similarity to the ϕ phase, we label it as the ϕ phase. STM data for the ϕ phase is shown in Figure S2(A). The FFT pattern of a defect-free part of the ϕ phase is given as an inset. Again, a hexagonal structure is observed. The FFT looks similar to the one in Figure 3(A) from the main text, again a centered cell can be selected. For the model in Figure S2(B), again mostly bridge sites were assumed, and less 4-fold hollow sites. This choice was made in order to account for the lack of striking height variations in the STM data. Next, a commonly observed feature in Figure S2 structure is the same. This, in combination with the similar FFT patterns, suggests that the ϕ phase is structurally and energetically very close to the ϕ phase. Furthermore, it is possible that the difference in the molecular tails-tip interactions due to the orientation of these phases contributes to their different appearance, while they are quite analogous to each other and simply rotational domains of the same phase.

Phase profiles
Profiles of the striped β and β phases are shown in Figure S3(A-D). From the height profiles we learn that only a single molecular row per stripe is of high enough apparent height to account for the monolayer step expected (0.2 nm). That is why, these rows were modeled on top of Au-adatom rows, as discussed in the main text. The width of the phases is also deduced from the width profiles. The β phase is 6.2 nm wide, a single stripe of this phase is 3. The profile graph is shown in the inset. With red arrows we mark the highest molecular rows, at which the height would be sufficient to account for the Au(001) monolayer step of 0.2 nm. (B) Width profile of the β phase. The profile graph is shown in the inset. The width of the phase (the whole unit cell) is 2w=6.2 nm. A width of a single stripe is w=3.1 nm. (C) Height profile of the β phase. The profile graph is shown in the inset. With red arrows we mark the highest molecular rows, at which the height would be sufficient to account for the Au(001) monolayer step of 0.2 nm. (D) Width profile of the β phase. The profile graph is shown in the inset. The width of the phase (the whole unit cell) is 2w=4.28 nm. A width of a single stripe is w=2.14 nm. (E) Profile across the hex reconstruction. The profile graph is shown as an inset. The width of a hex stripe is w=1.65 nm.

S6
wide. The β phase is 4.28 nm wide, a single stripe of this phase is 2.14 nm wide. A profile across the hex reconstruction is shown as well in (E). Having in mind the width of the hex reconstruction (1.65 mm), we learn that a single stripe of the β phase contains approximately twice the width of the hex reconstruction. A single stripe of the β phase is wider than the hex reconstruction, and less wide compared to two hex reconstruction stripes. The expected width of the hex reconstruction is 1.44 nm (perpendicular to the stripe direction, 6 atoms of the hex overlayer must fit on top of 5 atoms of the underlying unreconstructed substrate).
The fact that we measure a slightly wider hex stripe demonstrates the limitations of our beetle scanner. That is why, we made the decision to use the tolerances as given in Table   S1 when modeling the phases.

Computational results
In this section we present the results from the simulations addressed in the computational section from the main text.
The initial molecular configurations that we considered are shown in Figure S4

XPS results
The chemical nature of the decanethiol molecules on Au(001) was assessed by X-ray photoelectron spectroscopy, XPS (see Fig. S5). The S2p region of the XPS spectrum is shown.
Usually, the S2p3/2 core level peak for SAMs of thiols on Au can be decomposed into three components; (i) S1 at 161 eV binding energy (BE), associated with atomically adsorbed S7 sulfur, (ii) S2 at 162 eV BE related to S atoms chemisorbed on the metal surface through a thiolate bond in the thiol-Au interface and (iii) S3 at 163.5 eV BE, indicating physisorbed species. 1-3 In Fig. S5, two of these components are visible: S2 and S3; The S2p3/2 peak is located at 161.7 eV BE and the S2p1/2 peak at 162.9 eV BE. This is in good agreement with previous measurements of hexanethiol adsorption on Au(100). 1 The separation between the S2p3/2 and S2p1/2 peak is fixed to 1.2 eV which is the spin-orbit doublet separation.
The S3 component is located near 163.5 eV BE. This component is very broad and low in intensity, demonstrating the dominance of chemisorbed species over the physisorbed ones.